ClinVar Genomic variation as it relates to human health

The c.739C>T (p.Q247*) alteration, located in coding exon 5 of the TRIM63 gene, consists of a C to T substitution at nucleotide position 739. This changes the amino acid from a glutamine (Q) to a stop codon at amino acid position 247. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. Based on data from gnomAD, the T allele has an overall frequency of 0.068% (192/282876) total alleles studied. The highest observed frequency was 0.81% (84/10370) of Ashkenazi Jewish alleles. This variant has been identified in the homozygous state and compound heterozygous with another TRIM63 variant in multiple individuals with features consistent with TRIM63-related hypertrophic cardiomyopathy (Olivé, 2015; Jokela, 2019; Salazar-Mendiguchía, 2020; Andreeva, 2022). Induced expression of the TRIM63 p.Q247* alteration in the mouse heart was associated with cardiac hypertrophy, activation of the MTOR-S6K and calcineurin pathways, and expression of hypertrophic markers, which were normalized on turning off expression of the mutant protein (Chen, 2012). Functional analysis of the variant in HeLa cells and cardiac myocytes indicated a defect in E3 ligase activity as revealed by impaired auto-ubiquitination as well as ubiquitination and subsequent degradation of TRIM63 substrates, MYH6 and MYBPC3 (Chen, 2012). However it is important to note that these expression studies were performed using a cDNA construct which likely has different physiological effects than the genomic fragment (dominant negative vs. loss of function). Based on the available evidence, this alteration is classified as pathogenic.

Frequency: The variant is rare, observed in 192 alleles out of 282,876 (0.067874%) in the gnomAD2 reference population dataset (PM2_support). Frequency among cases: This variant has been reported in the literature in individuals affected with Hypertrophic Cardiomyopathy (PMID:24436435 , 32451364) (PS4). Variant type: Null variant in a gene where loss of function is probably mechanism of disease (PVS1). Clinical evidence: This variant has previously been described in ClinVar (VCV222849) with the following classifications: LB (1) / VUS (2) / P (1) / LP (1). Gene coverage: 100% of TRIM63 is covered with at least 10x.

Variant summary: TRIM63 c.739C>T (p.Gln247X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 0.0007 in 251478 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in TRIM63 causing Hypertrophic Cardiomyopathy (0.0007 vs 0.005), allowing no conclusion about variant significance. c.739C>T has been reported in the literature in individuals affected with Hypertrophic Cardiomyopathy (e.g. Chen_2013, Olive_2015, Jokela_2019, Salazar-Mendiguchia_2020, Andreeva_2022), primarily affecting homozygous and compound heterozygous individuals. Confirmed heterozygous carriers were unaffected (e.g. Ploski_2014, Olive_2015, Salazar-Mendiguchia_2020, Andreeva_2022). In vitro analysis of the variant in HeLa cells showed the variant completely abolished normal ubiquitination activity, which resulted in elevated levels of MYH6 and MYBPC3 levels (Chen_2013). In mice, transgenic 247* animals all showed evidence of ventricular wall thickening, which was reversed when the transgene was turned off (Chen_2013). The following publications have been ascertained in the context of this evaluation (PMID: 24436435, 32451364, 35273634, 22821932, 30372688, 25801283). ClinVar contains an entry for this variant (Variation ID: 222849). Based on the evidence outlined above, the variant was classified as pathogenic.

Based on the classification scheme VCGS_Germline_v1.3.5, this variant is classified as Likely pathogenic. Following criteria are met: 0102 - Loss of function is a likely mechanism of disease in this gene and is associated with hypertrophic cardiomyopathy (MONDO:0005045), TRIM63-related. (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v4) <0.01 for a recessive condition (810 heterozygotes, 4 homozygotes). (SP) 0708 - Other NMD-predicted variants comparable to the one identified in this case have conflicting previous evidence for pathogenicity. At least five other NMD-predicted variants have been reported, including in homozygous and compound heterozygous individuals with HCM, with VUS and pathogenic classifications (ClinVar, PMIDs: 38757491, 32451364). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been observed in multiple homozygous and compound heterozygous individuals with hypertrophic cardiomyopathy; heterozygous family members were unaffected (PMIDs: 30372688, 25801283, 32451364, 35273634, 37431535, 32659924). It has also been classified as likely benign, VUS and likely pathogenic/pathogenic by clinical laboratories in ClinVar. (SP) 0901 - This variant has strong evidence for segregation with disease. This variant has shown to segregate in homozygous and compound heterozygous families with HCM (PMIDs: 32451364, 25801283, 32659924). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

PP1, PP4, PS3_supporting, PS4, PVS1